Starting phenix.real_space_refine on Wed Sep 17 13:57:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y90_39065/09_2025/8y90_39065.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y90_39065/09_2025/8y90_39065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y90_39065/09_2025/8y90_39065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y90_39065/09_2025/8y90_39065.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y90_39065/09_2025/8y90_39065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y90_39065/09_2025/8y90_39065.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 40 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 6069 2.51 5 N 1413 2.21 5 O 1534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9058 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "A" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4516 Classifications: {'peptide': 565} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 544} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 26 Unusual residues: {' CL': 1, ' NA': 1, 'A1LX6': 1} Classifications: {'undetermined': 3, 'water': 5} Link IDs: {None: 7} Time building chain proxies: 2.24, per 1000 atoms: 0.25 Number of scatterers: 9058 At special positions: 0 Unit cell: (96.36, 86.87, 118.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 40 16.00 Na 1 11.00 O 1534 8.00 N 1413 7.00 C 6069 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 296.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2076 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 74.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'E' and resid 61 through 74 removed outlier: 3.758A pdb=" N PHE E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU E 66 " --> pdb=" O LYS E 62 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 105 Processing helix chain 'E' and resid 105 through 121 Processing helix chain 'E' and resid 125 through 134 removed outlier: 3.614A pdb=" N TRP E 128 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS E 129 " --> pdb=" O THR E 126 " (cutoff:3.500A) Proline residue: E 132 - end of helix Processing helix chain 'E' and resid 135 through 166 removed outlier: 4.094A pdb=" N TYR E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR E 151 " --> pdb=" O TYR E 147 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL E 154 " --> pdb=" O PHE E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 216 Processing helix chain 'E' and resid 234 through 253 Processing helix chain 'E' and resid 255 through 279 removed outlier: 4.132A pdb=" N LYS E 261 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL E 262 " --> pdb=" O THR E 258 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP E 264 " --> pdb=" O GLY E 260 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE E 265 " --> pdb=" O LYS E 261 " (cutoff:3.500A) Proline residue: E 270 - end of helix removed outlier: 3.973A pdb=" N PHE E 275 " --> pdb=" O TYR E 271 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL E 276 " --> pdb=" O PHE E 272 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 277 " --> pdb=" O VAL E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 295 removed outlier: 3.784A pdb=" N ILE E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 320 Processing helix chain 'E' and resid 324 through 333 removed outlier: 3.530A pdb=" N TYR E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 372 Processing helix chain 'E' and resid 385 through 398 Proline residue: E 392 - end of helix removed outlier: 3.614A pdb=" N THR E 397 " --> pdb=" O GLU E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 435 removed outlier: 3.557A pdb=" N TRP E 404 " --> pdb=" O GLY E 400 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL E 427 " --> pdb=" O GLY E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 441 Processing helix chain 'E' and resid 441 through 457 Processing helix chain 'E' and resid 457 through 462 Processing helix chain 'E' and resid 464 through 492 removed outlier: 3.985A pdb=" N VAL E 468 " --> pdb=" O GLY E 464 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU E 471 " --> pdb=" O TYR E 467 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP E 473 " --> pdb=" O LEU E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 509 Processing helix chain 'E' and resid 514 through 523 Processing helix chain 'E' and resid 523 through 539 Processing helix chain 'E' and resid 551 through 567 removed outlier: 3.811A pdb=" N ASN E 555 " --> pdb=" O PRO E 551 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER E 565 " --> pdb=" O ILE E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 567 through 580 Processing helix chain 'E' and resid 583 through 593 Processing helix chain 'E' and resid 598 through 603 removed outlier: 3.931A pdb=" N ALA E 602 " --> pdb=" O HIS E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 616 removed outlier: 4.052A pdb=" N TRP E 614 " --> pdb=" O GLN E 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 74 removed outlier: 3.954A pdb=" N PHE A 65 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.594A pdb=" N LEU A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.516A pdb=" N LEU A 116 " --> pdb=" O MET A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 135 through 167 removed outlier: 3.675A pdb=" N TYR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL A 154 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.632A pdb=" N GLU A 223 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 253 Processing helix chain 'A' and resid 255 through 284 removed outlier: 3.727A pdb=" N GLY A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LYS A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Proline residue: A 270 - end of helix Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.051A pdb=" N GLY A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 320 removed outlier: 4.486A pdb=" N TRP A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 309 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 338 through 373 removed outlier: 3.627A pdb=" N ALA A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.860A pdb=" N VAL A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 398 removed outlier: 3.894A pdb=" N LEU A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Proline residue: A 392 - end of helix Processing helix chain 'A' and resid 400 through 435 removed outlier: 3.769A pdb=" N ASP A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 439 Processing helix chain 'A' and resid 441 through 456 removed outlier: 3.608A pdb=" N PHE A 447 " --> pdb=" O LYS A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 494 removed outlier: 4.211A pdb=" N VAL A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 514 through 520 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 551 through 580 removed outlier: 3.824A pdb=" N ASN A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) Proline residue: A 570 - end of helix Processing helix chain 'A' and resid 583 through 593 Processing helix chain 'A' and resid 598 through 604 removed outlier: 4.375A pdb=" N ALA A 602 " --> pdb=" O HIS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 609 removed outlier: 3.507A pdb=" N PHE A 609 " --> pdb=" O ILE A 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 606 through 609' Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.030A pdb=" N TRP A 614 " --> pdb=" O GLN A 610 " (cutoff:3.500A) 551 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2647 1.34 - 1.46: 1907 1.46 - 1.57: 4730 1.57 - 1.69: 1 1.69 - 1.81: 62 Bond restraints: 9347 Sorted by residual: bond pdb=" C01 A1LX6 A 701 " pdb=" N02 A1LX6 A 701 " ideal model delta sigma weight residual 1.449 1.273 0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" C03 A1LX6 A 701 " pdb=" N02 A1LX6 A 701 " ideal model delta sigma weight residual 1.450 1.366 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C12 A1LX6 A 701 " pdb=" C13 A1LX6 A 701 " ideal model delta sigma weight residual 1.515 1.582 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C07 A1LX6 A 701 " pdb=" C08 A1LX6 A 701 " ideal model delta sigma weight residual 1.396 1.449 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" C11 A1LX6 A 701 " pdb=" C12 A1LX6 A 701 " ideal model delta sigma weight residual 1.398 1.449 -0.051 2.00e-02 2.50e+03 6.49e+00 ... (remaining 9342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 12534 1.77 - 3.53: 186 3.53 - 5.30: 26 5.30 - 7.06: 7 7.06 - 8.83: 1 Bond angle restraints: 12754 Sorted by residual: angle pdb=" N VAL E 74 " pdb=" CA VAL E 74 " pdb=" C VAL E 74 " ideal model delta sigma weight residual 106.21 109.57 -3.36 1.07e+00 8.73e-01 9.87e+00 angle pdb=" C ASP A 546 " pdb=" CA ASP A 546 " pdb=" CB ASP A 546 " ideal model delta sigma weight residual 110.81 115.78 -4.97 1.60e+00 3.91e-01 9.64e+00 angle pdb=" C LEU A 191 " pdb=" CA LEU A 191 " pdb=" CB LEU A 191 " ideal model delta sigma weight residual 110.92 115.83 -4.91 1.59e+00 3.96e-01 9.55e+00 angle pdb=" C12 A1LX6 A 701 " pdb=" C13 A1LX6 A 701 " pdb=" N02 A1LX6 A 701 " ideal model delta sigma weight residual 113.93 122.76 -8.83 3.00e+00 1.11e-01 8.66e+00 angle pdb=" N ASP A 546 " pdb=" CA ASP A 546 " pdb=" C ASP A 546 " ideal model delta sigma weight residual 111.11 107.69 3.42 1.20e+00 6.94e-01 8.14e+00 ... (remaining 12749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 4901 16.53 - 33.05: 223 33.05 - 49.58: 76 49.58 - 66.11: 20 66.11 - 82.63: 6 Dihedral angle restraints: 5226 sinusoidal: 1962 harmonic: 3264 Sorted by residual: dihedral pdb=" CA VAL E 374 " pdb=" C VAL E 374 " pdb=" N ASN E 375 " pdb=" CA ASN E 375 " ideal model delta harmonic sigma weight residual 180.00 152.69 27.31 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA TRP E 128 " pdb=" C TRP E 128 " pdb=" N LYS E 129 " pdb=" CA LYS E 129 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LYS E 373 " pdb=" C LYS E 373 " pdb=" N VAL E 374 " pdb=" CA VAL E 374 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1064 0.038 - 0.076: 304 0.076 - 0.114: 47 0.114 - 0.152: 3 0.152 - 0.189: 1 Chirality restraints: 1419 Sorted by residual: chirality pdb=" C06 A1LX6 A 701 " pdb=" C07 A1LX6 A 701 " pdb=" C14 A1LX6 A 701 " pdb=" O05 A1LX6 A 701 " both_signs ideal model delta sigma weight residual False 2.38 2.19 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA LEU A 269 " pdb=" N LEU A 269 " pdb=" C LEU A 269 " pdb=" CB LEU A 269 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA PRO A 570 " pdb=" N PRO A 570 " pdb=" C PRO A 570 " pdb=" CB PRO A 570 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.60e-01 ... (remaining 1416 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 477 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.88e+00 pdb=" C ALA E 477 " -0.049 2.00e-02 2.50e+03 pdb=" O ALA E 477 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY E 478 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 476 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C ALA E 476 " 0.048 2.00e-02 2.50e+03 pdb=" O ALA E 476 " -0.018 2.00e-02 2.50e+03 pdb=" N ALA E 477 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 475 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C PHE E 475 " 0.043 2.00e-02 2.50e+03 pdb=" O PHE E 475 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA E 476 " -0.015 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 235 2.71 - 3.26: 9740 3.26 - 3.81: 15390 3.81 - 4.35: 19083 4.35 - 4.90: 32295 Nonbonded interactions: 76743 Sorted by model distance: nonbonded pdb=" OH TYR E 205 " pdb=" O LYS E 373 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR E 332 " pdb=" OG1 THR E 429 " model vdw 2.202 3.040 nonbonded pdb=" O ALA E 328 " pdb=" OG SER E 331 " model vdw 2.236 3.040 nonbonded pdb=" O LEU E 471 " pdb=" OG1 THR E 474 " model vdw 2.253 3.040 nonbonded pdb=" O SER A 251 " pdb=" OG SER A 259 " model vdw 2.261 3.040 ... (remaining 76738 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 53 through 617) selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.540 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.176 9347 Z= 0.175 Angle : 0.565 8.828 12754 Z= 0.344 Chirality : 0.034 0.189 1419 Planarity : 0.004 0.038 1554 Dihedral : 11.765 82.634 3150 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 6.09 % Allowed : 8.19 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.22), residues: 1126 helix: -0.83 (0.17), residues: 758 sheet: None (None), residues: 0 loop : -1.76 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 216 TYR 0.008 0.001 TYR A 98 PHE 0.008 0.001 PHE E 475 TRP 0.009 0.001 TRP E 128 HIS 0.002 0.000 HIS A 228 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9347) covalent geometry : angle 0.56533 (12754) hydrogen bonds : bond 0.15051 ( 551) hydrogen bonds : angle 6.30655 ( 1638) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 313 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 152 TYR cc_start: 0.6618 (t80) cc_final: 0.5904 (t80) REVERT: E 173 TRP cc_start: 0.5954 (OUTLIER) cc_final: 0.4968 (m-90) REVERT: E 250 PHE cc_start: 0.7255 (m-80) cc_final: 0.6910 (t80) REVERT: E 314 GLN cc_start: 0.6721 (OUTLIER) cc_final: 0.6423 (mm110) REVERT: E 347 SER cc_start: 0.7763 (m) cc_final: 0.7296 (m) REVERT: A 111 TYR cc_start: 0.7911 (t80) cc_final: 0.7564 (t80) REVERT: A 122 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5884 (mt-10) REVERT: A 147 TYR cc_start: 0.7789 (m-10) cc_final: 0.7303 (m-10) REVERT: A 212 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7167 (mt-10) REVERT: A 263 VAL cc_start: 0.6406 (OUTLIER) cc_final: 0.6124 (m) REVERT: A 397 THR cc_start: 0.8075 (m) cc_final: 0.7710 (p) REVERT: A 418 ASP cc_start: 0.7875 (t0) cc_final: 0.7581 (t0) REVERT: A 490 ILE cc_start: 0.8208 (mt) cc_final: 0.7999 (mp) REVERT: A 519 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8344 (tt) REVERT: A 556 TRP cc_start: 0.6713 (m100) cc_final: 0.6213 (m100) REVERT: A 576 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6866 (tptt) outliers start: 58 outliers final: 12 residues processed: 354 average time/residue: 0.0881 time to fit residues: 44.3447 Evaluate side-chains 195 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 257 LYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 576 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.201858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.168400 restraints weight = 13904.617| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.27 r_work: 0.3947 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9347 Z= 0.137 Angle : 0.593 12.838 12754 Z= 0.301 Chirality : 0.040 0.209 1419 Planarity : 0.005 0.083 1554 Dihedral : 6.947 57.760 1264 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.88 % Allowed : 14.18 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.24), residues: 1126 helix: 0.34 (0.18), residues: 768 sheet: None (None), residues: 0 loop : -1.53 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 216 TYR 0.015 0.001 TYR A 575 PHE 0.020 0.001 PHE E 272 TRP 0.020 0.001 TRP E 80 HIS 0.007 0.001 HIS E 222 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9347) covalent geometry : angle 0.59282 (12754) hydrogen bonds : bond 0.04485 ( 551) hydrogen bonds : angle 4.72469 ( 1638) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 202 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: E 152 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6191 (t80) REVERT: E 173 TRP cc_start: 0.6049 (OUTLIER) cc_final: 0.4786 (m-90) REVERT: E 189 LYS cc_start: 0.6806 (mmtt) cc_final: 0.6538 (mptt) REVERT: E 250 PHE cc_start: 0.7731 (m-80) cc_final: 0.6860 (t80) REVERT: E 314 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6338 (mm-40) REVERT: E 347 SER cc_start: 0.7944 (m) cc_final: 0.7136 (m) REVERT: E 517 TRP cc_start: 0.6564 (m100) cc_final: 0.6157 (m100) REVERT: E 520 CYS cc_start: 0.4718 (m) cc_final: 0.4256 (p) REVERT: A 111 TYR cc_start: 0.8198 (t80) cc_final: 0.7755 (t80) REVERT: A 147 TYR cc_start: 0.8090 (m-10) cc_final: 0.7724 (m-10) REVERT: A 418 ASP cc_start: 0.8243 (t0) cc_final: 0.8005 (t0) REVERT: A 556 TRP cc_start: 0.6933 (m100) cc_final: 0.6415 (m100) REVERT: A 566 MET cc_start: 0.6410 (mtp) cc_final: 0.6065 (mtt) REVERT: A 576 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7162 (mmmt) outliers start: 56 outliers final: 24 residues processed: 236 average time/residue: 0.0812 time to fit residues: 27.8306 Evaluate side-chains 191 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 451 PHE Chi-restraints excluded: chain E residue 541 LYS Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 576 LYS Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 0.9980 chunk 12 optimal weight: 0.0020 chunk 91 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.195516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.159956 restraints weight = 13838.674| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.31 r_work: 0.3888 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9347 Z= 0.131 Angle : 0.594 12.511 12754 Z= 0.295 Chirality : 0.040 0.177 1419 Planarity : 0.004 0.042 1554 Dihedral : 6.104 57.687 1249 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.73 % Allowed : 16.28 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.25), residues: 1126 helix: 0.57 (0.18), residues: 761 sheet: None (None), residues: 0 loop : -1.16 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 81 TYR 0.019 0.001 TYR E 249 PHE 0.025 0.001 PHE A 445 TRP 0.038 0.001 TRP E 80 HIS 0.005 0.001 HIS E 222 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9347) covalent geometry : angle 0.59391 (12754) hydrogen bonds : bond 0.04250 ( 551) hydrogen bonds : angle 4.55222 ( 1638) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 152 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6347 (t80) REVERT: E 173 TRP cc_start: 0.6317 (OUTLIER) cc_final: 0.4867 (m-90) REVERT: E 189 LYS cc_start: 0.6895 (mmtt) cc_final: 0.6635 (mmtt) REVERT: E 250 PHE cc_start: 0.7653 (m-80) cc_final: 0.6743 (t80) REVERT: E 259 SER cc_start: 0.7509 (OUTLIER) cc_final: 0.6932 (t) REVERT: E 347 SER cc_start: 0.7656 (m) cc_final: 0.7230 (m) REVERT: E 518 ARG cc_start: 0.7379 (ptm160) cc_final: 0.6939 (ptm160) REVERT: A 111 TYR cc_start: 0.8149 (t80) cc_final: 0.7644 (t80) REVERT: A 147 TYR cc_start: 0.8160 (m-10) cc_final: 0.7782 (m-10) REVERT: A 342 ASP cc_start: 0.7481 (m-30) cc_final: 0.7002 (m-30) REVERT: A 418 ASP cc_start: 0.8146 (t0) cc_final: 0.7898 (t0) REVERT: A 556 TRP cc_start: 0.6947 (m100) cc_final: 0.6414 (m100) REVERT: A 588 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8101 (mm) outliers start: 45 outliers final: 26 residues processed: 212 average time/residue: 0.0749 time to fit residues: 23.5158 Evaluate side-chains 184 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 152 TYR Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 451 PHE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.189162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.154816 restraints weight = 14047.868| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.39 r_work: 0.3790 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9347 Z= 0.152 Angle : 0.598 11.214 12754 Z= 0.302 Chirality : 0.041 0.198 1419 Planarity : 0.004 0.062 1554 Dihedral : 5.581 54.336 1240 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.57 % Allowed : 16.81 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.25), residues: 1126 helix: 0.69 (0.19), residues: 762 sheet: None (None), residues: 0 loop : -0.95 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 216 TYR 0.020 0.002 TYR A 161 PHE 0.024 0.002 PHE E 272 TRP 0.024 0.001 TRP E 80 HIS 0.005 0.001 HIS E 441 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 9347) covalent geometry : angle 0.59804 (12754) hydrogen bonds : bond 0.04529 ( 551) hydrogen bonds : angle 4.52682 ( 1638) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 165 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: E 111 TYR cc_start: 0.7293 (t80) cc_final: 0.6988 (t80) REVERT: E 112 MET cc_start: 0.7732 (ttm) cc_final: 0.7487 (ttt) REVERT: E 113 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6798 (mt-10) REVERT: E 173 TRP cc_start: 0.6892 (OUTLIER) cc_final: 0.5980 (m-90) REVERT: E 189 LYS cc_start: 0.7120 (mmtt) cc_final: 0.6754 (mmtt) REVERT: E 250 PHE cc_start: 0.7735 (m-80) cc_final: 0.6740 (t80) REVERT: E 471 LEU cc_start: 0.5211 (OUTLIER) cc_final: 0.4772 (tt) REVERT: E 518 ARG cc_start: 0.7399 (ptm160) cc_final: 0.6922 (ptm160) REVERT: E 520 CYS cc_start: 0.4988 (m) cc_final: 0.4644 (p) REVERT: A 111 TYR cc_start: 0.8309 (t80) cc_final: 0.7555 (t80) REVERT: A 147 TYR cc_start: 0.8533 (m-10) cc_final: 0.8007 (m-10) REVERT: A 206 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7818 (mtpp) REVERT: A 391 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.6810 (m-10) REVERT: A 556 TRP cc_start: 0.7184 (m100) cc_final: 0.6542 (m100) outliers start: 53 outliers final: 32 residues processed: 205 average time/residue: 0.0807 time to fit residues: 24.2622 Evaluate side-chains 185 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 148 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 355 PHE Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 2 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.188208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.153833 restraints weight = 13942.301| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 2.42 r_work: 0.3767 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9347 Z= 0.143 Angle : 0.588 10.077 12754 Z= 0.296 Chirality : 0.040 0.173 1419 Planarity : 0.004 0.048 1554 Dihedral : 5.527 55.876 1240 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.94 % Allowed : 18.38 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.25), residues: 1126 helix: 0.82 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -1.06 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 81 TYR 0.017 0.001 TYR A 161 PHE 0.024 0.001 PHE E 329 TRP 0.014 0.001 TRP E 264 HIS 0.003 0.001 HIS A 280 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9347) covalent geometry : angle 0.58757 (12754) hydrogen bonds : bond 0.04454 ( 551) hydrogen bonds : angle 4.49263 ( 1638) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 163 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: E 111 TYR cc_start: 0.7388 (t80) cc_final: 0.7032 (t80) REVERT: E 173 TRP cc_start: 0.6966 (OUTLIER) cc_final: 0.6143 (m-90) REVERT: E 189 LYS cc_start: 0.7206 (mmtt) cc_final: 0.6845 (mmtt) REVERT: E 250 PHE cc_start: 0.7771 (m-80) cc_final: 0.6740 (t80) REVERT: E 471 LEU cc_start: 0.5047 (OUTLIER) cc_final: 0.4542 (tt) REVERT: E 518 ARG cc_start: 0.7438 (ptm160) cc_final: 0.6943 (ptm160) REVERT: E 520 CYS cc_start: 0.4930 (m) cc_final: 0.4592 (p) REVERT: A 147 TYR cc_start: 0.8635 (m-10) cc_final: 0.8067 (m-10) REVERT: A 206 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7844 (mtpp) REVERT: A 391 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6851 (m-10) REVERT: A 556 TRP cc_start: 0.7206 (m100) cc_final: 0.6514 (m100) REVERT: A 566 MET cc_start: 0.7683 (mtp) cc_final: 0.7468 (mtp) outliers start: 47 outliers final: 29 residues processed: 195 average time/residue: 0.0826 time to fit residues: 23.7607 Evaluate side-chains 180 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 166 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 531 PHE Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 17 optimal weight: 0.0370 chunk 93 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.192806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.157989 restraints weight = 13963.719| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 2.29 r_work: 0.3793 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9347 Z= 0.124 Angle : 0.591 12.965 12754 Z= 0.292 Chirality : 0.040 0.191 1419 Planarity : 0.004 0.041 1554 Dihedral : 5.411 56.715 1239 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.89 % Allowed : 20.17 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.25), residues: 1126 helix: 0.93 (0.19), residues: 765 sheet: None (None), residues: 0 loop : -0.96 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 440 TYR 0.018 0.001 TYR A 161 PHE 0.020 0.001 PHE A 362 TRP 0.012 0.001 TRP E 264 HIS 0.002 0.000 HIS E 598 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9347) covalent geometry : angle 0.59146 (12754) hydrogen bonds : bond 0.04176 ( 551) hydrogen bonds : angle 4.42703 ( 1638) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: E 111 TYR cc_start: 0.7330 (t80) cc_final: 0.6976 (t80) REVERT: E 189 LYS cc_start: 0.7157 (mmtt) cc_final: 0.6843 (mmtt) REVERT: E 250 PHE cc_start: 0.7574 (m-80) cc_final: 0.6628 (t80) REVERT: E 471 LEU cc_start: 0.4852 (OUTLIER) cc_final: 0.4335 (tt) REVERT: E 518 ARG cc_start: 0.7364 (ptm160) cc_final: 0.6868 (ptm160) REVERT: A 147 TYR cc_start: 0.8376 (m-10) cc_final: 0.7883 (m-10) REVERT: A 556 TRP cc_start: 0.7002 (m100) cc_final: 0.6457 (m100) REVERT: A 566 MET cc_start: 0.7518 (mtp) cc_final: 0.7300 (mtp) outliers start: 37 outliers final: 30 residues processed: 191 average time/residue: 0.0871 time to fit residues: 24.1049 Evaluate side-chains 181 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 451 PHE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 23 optimal weight: 0.0010 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.189589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.155384 restraints weight = 13976.313| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.20 r_work: 0.3791 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9347 Z= 0.128 Angle : 0.599 12.139 12754 Z= 0.296 Chirality : 0.040 0.192 1419 Planarity : 0.004 0.049 1554 Dihedral : 5.308 57.268 1237 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.41 % Allowed : 20.27 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.25), residues: 1126 helix: 0.94 (0.19), residues: 768 sheet: None (None), residues: 0 loop : -0.91 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 216 TYR 0.021 0.001 TYR A 391 PHE 0.023 0.001 PHE A 362 TRP 0.013 0.001 TRP E 264 HIS 0.002 0.001 HIS E 598 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9347) covalent geometry : angle 0.59893 (12754) hydrogen bonds : bond 0.04223 ( 551) hydrogen bonds : angle 4.42432 ( 1638) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 0.401 Fit side-chains REVERT: E 111 TYR cc_start: 0.7383 (t80) cc_final: 0.7009 (t80) REVERT: E 133 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7768 (m-10) REVERT: E 173 TRP cc_start: 0.7186 (OUTLIER) cc_final: 0.6476 (m-90) REVERT: E 189 LYS cc_start: 0.7153 (mmtt) cc_final: 0.6812 (mmtt) REVERT: E 250 PHE cc_start: 0.7678 (m-80) cc_final: 0.6674 (t80) REVERT: E 264 TRP cc_start: 0.5692 (t60) cc_final: 0.5437 (t60) REVERT: E 471 LEU cc_start: 0.4951 (OUTLIER) cc_final: 0.4414 (tt) REVERT: E 518 ARG cc_start: 0.7424 (ptm160) cc_final: 0.6931 (ptm160) REVERT: A 147 TYR cc_start: 0.8559 (m-10) cc_final: 0.8076 (m-10) REVERT: A 207 PHE cc_start: 0.7829 (m-80) cc_final: 0.7314 (m-80) REVERT: A 299 PHE cc_start: 0.7998 (m-80) cc_final: 0.7789 (m-80) REVERT: A 391 TYR cc_start: 0.7049 (OUTLIER) cc_final: 0.6536 (m-10) REVERT: A 556 TRP cc_start: 0.7186 (m100) cc_final: 0.6515 (m100) REVERT: A 566 MET cc_start: 0.7671 (mtp) cc_final: 0.7460 (mtp) outliers start: 42 outliers final: 34 residues processed: 188 average time/residue: 0.0877 time to fit residues: 23.9796 Evaluate side-chains 186 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 451 PHE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 chunk 14 optimal weight: 0.0770 chunk 49 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.191858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.154286 restraints weight = 13873.727| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.34 r_work: 0.3789 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9347 Z= 0.131 Angle : 0.618 14.724 12754 Z= 0.303 Chirality : 0.041 0.217 1419 Planarity : 0.004 0.045 1554 Dihedral : 5.314 57.871 1237 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.73 % Allowed : 20.90 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.25), residues: 1126 helix: 0.99 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -0.90 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 216 TYR 0.020 0.001 TYR A 391 PHE 0.031 0.001 PHE A 408 TRP 0.011 0.001 TRP E 264 HIS 0.006 0.001 HIS E 280 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9347) covalent geometry : angle 0.61840 (12754) hydrogen bonds : bond 0.04234 ( 551) hydrogen bonds : angle 4.41995 ( 1638) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.341 Fit side-chains REVERT: E 111 TYR cc_start: 0.7334 (t80) cc_final: 0.6935 (t80) REVERT: E 133 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7664 (m-10) REVERT: E 189 LYS cc_start: 0.7112 (mmtt) cc_final: 0.6835 (mmtt) REVERT: E 250 PHE cc_start: 0.7477 (m-80) cc_final: 0.6605 (t80) REVERT: E 264 TRP cc_start: 0.5712 (t60) cc_final: 0.5420 (t60) REVERT: E 332 TYR cc_start: 0.6935 (m-80) cc_final: 0.6602 (m-10) REVERT: E 471 LEU cc_start: 0.4751 (OUTLIER) cc_final: 0.4219 (tt) REVERT: E 518 ARG cc_start: 0.7439 (ptm160) cc_final: 0.6961 (ptm160) REVERT: A 147 TYR cc_start: 0.8371 (m-10) cc_final: 0.7971 (m-10) REVERT: A 207 PHE cc_start: 0.7717 (m-80) cc_final: 0.7262 (m-80) REVERT: A 391 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.6338 (m-10) REVERT: A 556 TRP cc_start: 0.7046 (m100) cc_final: 0.6463 (m100) REVERT: A 566 MET cc_start: 0.7612 (mtp) cc_final: 0.7411 (mtp) outliers start: 45 outliers final: 36 residues processed: 190 average time/residue: 0.0832 time to fit residues: 22.8823 Evaluate side-chains 192 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 451 PHE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 24 optimal weight: 0.0470 chunk 85 optimal weight: 0.9980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.192820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.158211 restraints weight = 13900.020| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.22 r_work: 0.3811 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3684 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9347 Z= 0.124 Angle : 0.608 13.619 12754 Z= 0.297 Chirality : 0.040 0.183 1419 Planarity : 0.004 0.043 1554 Dihedral : 5.317 58.641 1237 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.52 % Allowed : 21.22 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.25), residues: 1126 helix: 1.05 (0.19), residues: 766 sheet: None (None), residues: 0 loop : -0.85 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 216 TYR 0.019 0.001 TYR A 391 PHE 0.025 0.001 PHE A 408 TRP 0.010 0.001 TRP E 264 HIS 0.003 0.001 HIS E 222 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9347) covalent geometry : angle 0.60833 (12754) hydrogen bonds : bond 0.04120 ( 551) hydrogen bonds : angle 4.42020 ( 1638) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 0.339 Fit side-chains REVERT: E 107 MET cc_start: 0.7116 (mmm) cc_final: 0.6599 (tpt) REVERT: E 111 TYR cc_start: 0.7371 (t80) cc_final: 0.6955 (t80) REVERT: E 133 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7677 (m-10) REVERT: E 189 LYS cc_start: 0.7069 (mmtt) cc_final: 0.6749 (mmtt) REVERT: E 250 PHE cc_start: 0.7566 (m-80) cc_final: 0.6640 (t80) REVERT: E 264 TRP cc_start: 0.5684 (t60) cc_final: 0.5410 (t60) REVERT: E 332 TYR cc_start: 0.6989 (m-80) cc_final: 0.6577 (m-10) REVERT: E 471 LEU cc_start: 0.4852 (OUTLIER) cc_final: 0.4317 (tt) REVERT: E 518 ARG cc_start: 0.7484 (ptm160) cc_final: 0.7007 (ptm160) REVERT: A 147 TYR cc_start: 0.8500 (m-10) cc_final: 0.8049 (m-10) REVERT: A 207 PHE cc_start: 0.7877 (m-80) cc_final: 0.7325 (m-80) REVERT: A 391 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6608 (m-10) REVERT: A 556 TRP cc_start: 0.7205 (m100) cc_final: 0.6541 (m100) REVERT: A 566 MET cc_start: 0.7636 (mtp) cc_final: 0.7429 (mtp) outliers start: 43 outliers final: 35 residues processed: 186 average time/residue: 0.0744 time to fit residues: 20.9222 Evaluate side-chains 185 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 370 HIS Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 451 PHE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 48 optimal weight: 0.0000 chunk 44 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.190588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.152573 restraints weight = 13947.130| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.30 r_work: 0.3759 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9347 Z= 0.143 Angle : 0.643 13.444 12754 Z= 0.313 Chirality : 0.041 0.197 1419 Planarity : 0.004 0.039 1554 Dihedral : 5.377 59.215 1237 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.41 % Allowed : 21.64 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.25), residues: 1126 helix: 0.99 (0.19), residues: 778 sheet: None (None), residues: 0 loop : -0.71 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 216 TYR 0.016 0.001 TYR A 391 PHE 0.024 0.001 PHE A 362 TRP 0.011 0.001 TRP A 80 HIS 0.003 0.001 HIS E 598 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9347) covalent geometry : angle 0.64253 (12754) hydrogen bonds : bond 0.04353 ( 551) hydrogen bonds : angle 4.44962 ( 1638) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.283 Fit side-chains REVERT: E 107 MET cc_start: 0.7039 (mmm) cc_final: 0.6405 (tpt) REVERT: E 111 TYR cc_start: 0.7393 (t80) cc_final: 0.6920 (t80) REVERT: E 133 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7579 (m-10) REVERT: E 189 LYS cc_start: 0.7051 (mmtt) cc_final: 0.6754 (mmtt) REVERT: E 250 PHE cc_start: 0.7511 (m-80) cc_final: 0.6580 (t80) REVERT: E 332 TYR cc_start: 0.6991 (m-80) cc_final: 0.6633 (m-10) REVERT: E 471 LEU cc_start: 0.4765 (OUTLIER) cc_final: 0.4214 (tt) REVERT: E 518 ARG cc_start: 0.7482 (ptm160) cc_final: 0.6983 (ptm160) REVERT: A 147 TYR cc_start: 0.8378 (m-10) cc_final: 0.8029 (m-10) REVERT: A 391 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.6625 (m-10) REVERT: A 556 TRP cc_start: 0.7122 (m100) cc_final: 0.6504 (m100) outliers start: 42 outliers final: 35 residues processed: 181 average time/residue: 0.0822 time to fit residues: 21.9340 Evaluate side-chains 179 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 133 PHE Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 173 TRP Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 196 LEU Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 349 ILE Chi-restraints excluded: chain E residue 367 TYR Chi-restraints excluded: chain E residue 370 HIS Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain E residue 451 PHE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 543 LEU Chi-restraints excluded: chain E residue 588 LEU Chi-restraints excluded: chain E residue 598 HIS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 167 PHE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 593 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 0.0020 chunk 107 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.189179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.153628 restraints weight = 13738.385| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.21 r_work: 0.3736 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9347 Z= 0.156 Angle : 0.649 13.291 12754 Z= 0.320 Chirality : 0.042 0.193 1419 Planarity : 0.004 0.039 1554 Dihedral : 5.189 59.751 1237 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.10 % Allowed : 21.64 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.25), residues: 1126 helix: 1.06 (0.19), residues: 764 sheet: None (None), residues: 0 loop : -0.83 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 216 TYR 0.016 0.001 TYR A 391 PHE 0.025 0.001 PHE A 362 TRP 0.025 0.001 TRP E 264 HIS 0.003 0.001 HIS E 598 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9347) covalent geometry : angle 0.64876 (12754) hydrogen bonds : bond 0.04562 ( 551) hydrogen bonds : angle 4.51106 ( 1638) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 2645.50 seconds wall clock time: 45 minutes 40.68 seconds (2740.68 seconds total)